NDLI: Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness

Content Provider	Springer Nature Link
Author	Katyal, Isha Chaban, Bonnie Hill, Janet E.
Copyright Year	2015
Abstract	Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.
Starting Page	917
Ending Page	930
Page Count	14
File Format	PDF
ISSN	00953628
Journal	Microbial Ecology
Volume Number	72
Issue Number	4
e-ISSN	1432184X
Language	English
Publisher	Springer US
Publisher Date	2015-11-14
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Enterococcus hirae Ecotype Genome Competitive fitness index cpn60 Microbiology Ecology Microbial Ecology Geoecology/Natural Processes Nature Conservation Water Quality/Water Pollution
Content Type	Text
Resource Type	Article
Subject	Soil Science Ecology Ecology, Evolution, Behavior and Systematics

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